Hi Seren,
This is very strange. Are you certain that all the bugfixes applied
correctly? Were there any error messages during the patching? - the reason
you get fort.16 is that that is the unit used to write restart files.
Normally a file is opened and the unit pointed to a filename. You get the
default filename of fort.16 when the write occurs on a file that has not
been opened. Hence the restart file is closed when it is doing the write
which suggests to me that something is corrupt in the source code.
Do you have the original AMBER 11 and AmberTools 1.5 tar files? If you do
then you might want to try starting from a completely clean directory and
applying the bugfixes again (both amber and AmberTools) from scratch. It
might be quicker than trying to track down what went wrong previously.
All the best
Ross
> -----Original Message-----
> From: Seren Soner [mailto:seren.soner.gmail.com]
> Sent: Friday, July 13, 2012 6:44 AM
> To: AMBER Mailing List
> Subject: [AMBER] no restart file from pmemd.cuda in Amber 11
>
> Dear All,
>
> I have installed the final version of Amber 11, with all the bugfixes
> for both AmberTools 1.5 and Amber 11 itself. However, when I run
> pmemd.cuda, the restart file does not exist, but instead, there is a
> fort.16 file, very similar to the structure of restart file:
>
> 57554
> 62.6224520 33.2667655 16.8053255 62.5905991 32.3885900
> 16.2838384
> 63.5297068 33.7019482 16.6271135 61.8798230 33.8253635
> 16.3817990
> 62.3808115 32.9934161 18.2527516 62.9504305 32.1037091
> 18.5308745
> 62.9082214 34.1630195 19.1157645 62.2458675 34.3271875
> 19.9668928
> 62.9104991 35.0781751 18.5228503 64.3270737 33.8930776
> 19.6589332
> 64.9828308 33.5857061 18.8464886 64.2848324 33.0771144
> 20.3810183
> 64.9278300 35.1342910 20.3401949 64.2640329 35.4574561
> 21.1434712
> 65.0147031 35.9314095 19.6012539 66.3180777 34.8342963
> 20.9168274
> 67.0006435 34.5960489 20.0970415 66.2452251 33.9541394
> 21.5594070
> 66.8660280 35.9637909 21.7070618 67.7669238 35.7166182
> 22.1083976
> ...
>
> On top of my output file, I also can see that the restart file address
> is obtained from the argument:
>
> | RESTRT: /home/../xxx.rst
>
> I have compiled Amber 11 using Intel compilers, and since I already
> have patched for bugfix.22 and bugfix.23, what could be the problem ?
>
> Best regards,
> Seren Soner
>
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Received on Fri Jul 13 2012 - 07:00:04 PDT
